#! /bin/bash
#$ -q 1-day
#$ -l h_vmem=15G
#$ -M prodduturi.naresh@mayo.edu
#$ -m a
#$ -V
#$ -cwd
dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-11954
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-19018
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-24810
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-35957
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-40349
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-9593
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-13712
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-19864
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-35330
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-35959
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-GEOD-7696
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133_Plus_2
array=E-MEXP-2283
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_plus2  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133A
array=E-GEOD-2487
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_hguA  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HG-U133A
array=E-GEOD-33710
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_hguA  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt

dir=/data4/bsi/bioinf_ext1/s113890.senescence/HT_HG-U133A
array=E-GEOD-16058
perl perl_merge.pl -INPUT_FILE_LIST $dir/$array/file -REF_FILE /data4/bsi/bioinf_ext1/s113890.senescence/code_merge/reference_hguA  -TEMP  $dir/$array/temp -OUTPUT $dir/$array/combined_file.txt
